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shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

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Journal of Genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie Xuan-An Zhu Zijing Xie Jianfeng Lin Lin Li Wenli Tang Rui Wang Lin Deng yufan Liao Bingdong Liu Yantong Cai Qianwen Wang Shuangbin Xu guangchuang yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary *** a relaxed molecular clock model better aligns with the complexities of *** root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic *** its utility,there remains a lack of corresponding software implementations for broader *** address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://***/yuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

关键词： Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal

Reducing language barriers, promoting information absorption, and communication using fanyi

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中华医学杂志(英文版) 2024年第16期137卷 2024 Jul 22页

作者： Wang Difei Chen Guannan Li Lin Wen Shaodi Xie Zijing Luo Xiao Zhan Li Xu Shuangbin Li Junrui Wang Rui Wang Qianwen yu guangchuang Nanfang Hospital Southern Medical University Guangzhou Guangdong China Department of Bioinformatics School of Basic Medical Sciences Southern Medical University Guangzhou Guangdong China Comprehensive Technology Center of Lianyungang Customs Lianyungang Jiangsu China Department of Oncology The Affiliated Cancer Hospital of Nanjing Medical University &amp Jiangsu Cancer Hospital Nanjing Jiangsu China Department of Laboratory Medicine Microbiome Medicine Center Zhujiang Hospital Southern Medical University Guangzhou Guangdong China

Interpreting genes of interest is essential for identifying molecular mechanisms, but acquiring such information typically involves tedious manual retrieval. To streamline this process, thefanyi package offers tools to retrieve gene information from sources like National Center for Biotechnology Information (NCBI), significantly enhancing accessibility. Additionally, understanding the latest research advancements and sharing achievements are crucial for junior researchers. However, language barriers often restrict knowledge absorption and career development. To address these challenges, we developed thefanyi package, which leverages artificial intelligence (AI)-driven online translation services to accurately translate among multiple languages. This dual functionality allows researchers to quickly capture and comprehend information, promotes a multilingual environment, and fosters innovation in academic community. Meanwhile, the translation functions are versatile and applicable beyond biomedicine research to other domains as well. Thefanyi package is freely available at https://***/yuLab-SMU/fanyi.

关键词： Multilingualism Communication barriers Translating Artificial intelligence Single-cell analysis Gene expression profiling Biological markers

MicrobiotaProcess:A comprehensive R package for deep mining microbiome

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The Innovation 2023年第2期4卷 48-58,47页

作者： Shuangbin Xu Li Zhan Wenli Tang Qianwen Wang Zehan Dai Lang Zhou Tingze Feng Meijun Chen Tianzhi Wu Erqiang Hu guangchuang yu Division of Laboratory Medicine Microbiome Medicine CenterZhujiang HospitalSouthern Medical UniversityGuangzhou 510515China Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China

The data output from microbiome research is growing at an accelerating rate,yet mining the data quickly and efficiently remains *** is still a lack of an effective data structure to represent and manage data,as well as flexible and composable analysis *** response to these two issues,we designed and developed the MicrobiotaProcess *** provides a comprehensive data structure,MPSE,to better integrate the primary and intermediate data,which improves the integration and exploration of the downstream *** this data structure,the downstream analysis tasks are decomposed and a set of functions are designed under a tidy *** functions independently perform simple tasks and can be combined to perform complex tasks.

关键词： methods. structure integrate

clusterProfiler 4.0:A universal enrichment tool for interpreting omics data

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The Innovation 2021年第3期2卷 51-61页

作者： Tianzhi Wu Erqiang Hu Shuangbin Xu Meijun Chen Pingfan Guo Zehan Dai Tingze Feng Lang Zhou Wenli Tang Li Zhan Xiaocong Fu Shanshan Liu Xiaochen Bo guangchuang yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Department of Biotechnology Beijing Institute of Radiation MedicineBeijing 100850China Guangdong Provincial Key Laboratory of Proteomics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Microbiome Medicine Center Department of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou 510515China

Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life *** is crucial for this type of tool to use the latest annotation databases for as many organisms as *** meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler *** package has been enhanced considerably compared with its original version published 9 years *** new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online *** also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and *** new features include gene set enrichment analysis and comparison of enrichment results from multiple gene *** anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.

关键词： clusterProfiler biological knowledge mining functional analysis enrichment analysis visualization

组蛋白赖氨酸去甲基化酶家族在膀胱癌中的表达模式及其潜在作用:基于多组学分析

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南方医科大学学报 2022年第12期42卷 1822-1831页

作者：付小聪余光创郭艳芳南方医科大学基础医学院生物信息学系广东广州510515

目的探讨19个组蛋白赖氨酸去甲基化酶(KDMs)在膀胱癌多组学中的表达模式与潜在作用。方法本研究使用UALCAN和GSCALite分析来自TCGA的膀胱癌样本的KDMs的转录表达和甲基化水平、体细胞变异多组学高通量测序数据。使用Kaplan Meier-Plotte... 详细信息

目的探讨19个组蛋白赖氨酸去甲基化酶(KDMs)在膀胱癌多组学中的表达模式与潜在作用。方法本研究使用UALCAN和GSCALite分析来自TCGA的膀胱癌样本的KDMs的转录表达和甲基化水平、体细胞变异多组学高通量测序数据。使用Kaplan Meier-Plotter和Assistant for clinical bioinformatics探讨KDMs的表达对BLCA样本的预后影响。利用Timer和GSCALite分析KDMs在膀胱癌中的免疫浸润和药物敏感性。结果分析结果首先揭示了KDMs在膀胱癌多组学中的表达特征,并不是所有KDMs都具有一致的表达模式。转录组数据分析显示KDM1A/1B/2B/4A/4B/5B/5C的表达上调(P<0.05),而KDM3B/6B/7C的表达下调。甲基化水平差异分析显示KDM1A/3B/4A/4B/4C/5A/5B/5C/7B的甲基化水平下调,而KDM7C甲基化水平上调(P<0.05)。相关性分析显示,14个KDMs家族成员的转录水平与甲基化水平呈负相关,其中KDM1A最显著。突变分析显示,KDM6A非同义突变频率最高,突变种类最多,且与其它KDMs的非同义突变具有互补性。生存分析显示,KDM3A/4C/5D/6A/7B对BLCA患者总生存率具有保护性作用,而KDM3B/5B/5C对BLCA患者无复发生存率具有危险性影响。综合预后模型证实KDM4C/6A/7B具有膀胱癌预后生物标志物的潜在作用,其表达与BLCA患者免疫浸润呈正相关。药物敏感性分析显示,KDM2B/3B/4B/4C/5A与大多数抗癌药物呈负相关,而KDM2B/4B与6种抗癌药物呈正相关(P<0.05)。结论本研究系统性地揭示了KDMs基因家族在膀胱癌中的高突变互补性、过表达与低甲基化负相关性的特征,并与膀胱癌预后、免疫浸润和药物敏感性密切相关。

关键词：膀胱癌组蛋白赖氨酸去甲基化酶多组学

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分段数对生长管过饱和环境特征的影响

东南大学学报（自然科学版） 2018年第2期48卷 226-231页

作者：于燕张军陈广闯徐俊超闾荔钟辉东南大学能源热转换及其过程测控教育部重点实验室南京210096

为了研究多段式生长管中水汽相变条件下不同构建方式及初始参数等操作条件下,生长管分段数对形成的过饱和环境特征的影响,利用变物性参数传热传质模型对多段式生长管中2种过饱和构建方式,即低温饱和气流与高温热水相接触(方式1)和高温... 详细信息

为了研究多段式生长管中水汽相变条件下不同构建方式及初始参数等操作条件下,生长管分段数对形成的过饱和环境特征的影响,利用变物性参数传热传质模型对多段式生长管中2种过饱和构建方式,即低温饱和气流与高温热水相接触(方式1)和高温饱和气体与低温冷水相接触(方式2)及不同初始参数下形成的过饱和度分布进行了计算,分析不同分段数下形成的过饱和度分布均匀性和过饱和度水平.计算结果表明:在温差(进气温度与管壁温度)为35 K,生长管总长度为120 cm时,方式1下生长管的分段数为10时过饱和度分布均匀性较好且过饱和度水平较高;方式2下生长管的分段数为3时过饱和度分布均匀性较好且过饱和度水平较高,方式2下生长管的分段数为10时过饱和度均匀性最佳,但整体过饱和水平下降;要达到均匀化和过饱和度水平较高的过饱和度分布,随着生长管总长度的增加,2种方式下生长管的分段数都要有所增加;而随着温差的增加,方式1的分段数需稍有增加,方式2的分段数则需减少.

关键词：细颗粒物多段式生长管过饱和度传热传质